mikropml
software
machine learning
R
User-Friendly R Package for Supervised Machine Learning Pipelines
| Co-author and maintainer |
Bioinformatician developing open source software
Contact: sovacool [at] umich.edu
View a PDF version of my CV: https://sovacool.dev/latex-cv/vitae_KLS.pdf
| Dates | Degree | Institution |
|---|---|---|
| 2018-2023 | PhD Bioinformatics |
University of Michigan, Dept. of Computational Medicine and Bioinformatics Advisor: Patrick D. Schloss |
| 2014-2018 | BS Biology |
University of Kentucky, Dept. of Biology Minor: Computer Science |
| Dates | Title | Lab | Projects |
|---|---|---|---|
| 2023-present | Bioinformatics Software Engineer II | Frederick National Laboratory for Cancer Research | Develop and maintain open source bioinformatics workflows on the CCR Collaborative Bioinformatics Resource core team to support researchers at the National Cancer Institute. |
| 2019-2023 | Graduate Student Researcher |
Schloss Lab, Dept. of Microbiology and Immunology, University of Michigan |
- Developed, benchmarked, and maintained bioinformatics workflows and software packages in R & Python. - Built machine learning pipelines for human gut microbiome classification problems in colorectal cancer and C. difficile infection. - Published findings as reproducible papers in open access journals. - Collaborated with other scientists on microbiome projects. - Mentored junior lab members. |
| 2018-2019 | Rotation Student Researcher |
Program in Biomedical Sciences, University of Michigan |
Worked in several different bioinformatics labs to find the best mentorship fit. |
| 2015-2018 | Undergraduate Lab Assistant |
Moseley Bioinformatics Lab, Dept. of Molecular and Cellular Biochemistry, University of Kentucky |
- Developed a Python package for comparative genomics. Identified sets of orthologous and paralogous gene products to facilitate collinearity analysis and detection of gene duplication events. |
| 2016-2018 | BIO395 Independent Research Student |
Weisrock Lab, Dept. of Biology, University of Kentucky |
- Developed bash scripts and a SNP calling pipeline in Snakemake. - Population structure analysis of the Ambystoma tigrinum species complex. - Bayesian species delimitation of the Desmognathus fuscus species complex. |
| 2015-2016 | Undergraduate Lab Assistant |
Jaromczyk Lab, Dept. of Computer Science, University of Kentucky |
- Maintained the Epichloë festucae genome project database. - Analyzed RNA-seq data of Chenopodium quinoa and coffee ringspot virus. |
| Dates | Title | Organization | Projects |
|---|---|---|---|
| 2019-2022 | Executive Committee Member: Open Source Technical Lead | Girls Who Code at U-M DCMB | - Plan, apply for funding, develop curriculum, and maintain resources to teach introductory Python programming & data science to young women+. - Facilitate collaborative development and maintenance of our open source teaching resources. - Organize our year-round Club and annual Data Science Summer Experience for high school women+. |
| 2019-2022 | Organizer and Maintainer | U-M Carpentries | - Co-lead development & maintenance of a curriculum for workshops teaching programming skills for reproducible research. - Maintain the website, develop curriculum, and organize workshops. - Collaborate with U-M Women in Science and Engineering to organize workshops for women+. |
| 2021-2023 | Mentor | Schloss Lab | Mentor an undergraduate student in building reproducible machine learning models to predict C. difficile infection severity from gut microbiome composition. |
| 2021-2022 | CoderSpaces co-host | U-M ISR Data Science Hub | Hold office hours at a weekly virtual help session for data science practitioners |
| 2021 | Peer reviewer | PLOS ONE (1) | |
| 2019-2021 | Graduate Student Coordinator | U-M Data Analysis Networking Group | - Organize monthly meetings & a one-day symposium for researchers to sharpen their data analysis skills. - Apply for funding through a Rackham Interdisciplinary Workshop grant. |
| 2009-present | Volunteer Sound Engineer | various churches and non-profit organizations | Mix FOH, monitors, recording, and live stream. |
| dates | Title | Organization | Event(s) |
|---|---|---|---|
| Mar 2019 | Capstone Activity Leader | Females Excelling More in Math, Engineering, & the Sciences | Binary Numbers through Ozobots with GWC at U-M DCMB |
| Apr 2019 | DNA Day Ambassador | Michigan DNA Day | Epigenetics & Scientific Journeys |
| 2019-2022 | Facilitator & Capstone Project Mentor | Girls Who Code at U-M DCMB | Weekly Club during the school year and week-long Summer Experience for high schoolers to learn Python for data science |
| Jan-Apr 2023 | Graduate Student Instructor | BIOINF 576: Tool Development for Bioinformatics. Dept. of Computational Medicine & Bioinformatics | Develop curriculum and teach students the principles of software development in R & Python. Topics: software design, implementation, testing, documentation, issue tracking, peer review, and release. |
| Jun 2022 | Instructor | Intro to R & RNA-Seq Workshop for ASM Microbe conference attendees | |
| 2012-2018 | Tutor | freelance | for high school and college students in Biology, Calculus, Chemistry, Computer Science, and Bioinformatics. |
| 2018-present | Workshop Instructor & Helper | U-M Carpentries | 2-day Software Carpentry workshops teaching computational skills for reproducible research |
| Mar 2019 | Workshop helper | Graduate Society of Black Engineers and Scientists | Data Visualization with Python Workshop |
| Date | Title | Organization | Location |
|---|---|---|---|
| Jan 2020 | Building Tidy Tools workshop at rstudio::conf | Rstudio, PBC | San Francisco, CA |
| Dec 2019 | Winter School in Research Software Engineering | US Research Software Sustainability Institute | Seattle, WA |
| Jun 2019 | Software Carpentry Instructor Training | The Carpentries | University of Michigan |
| May 2019 | PyCon Education Summit & Conference | The Python Software Foundation | Cleveland, OH |
| Apr 2019 | MICROBIOL 612.2 | Riffomonas Minimal R Workshop | University of Michigan |
| Dates | Title | Institution | Amount |
|---|---|---|---|
| 2022 | Conference Travel Grant |
Rackham Graduate School University of Michigan |
$900 |
| 2020-2021 | Rackham Interdisciplinary Workshop Grant |
Rackham Graduate School University of Michigan |
$500 |
| 2020 | Conference Travel Grant |
Rackham Graduate School University of Michigan |
$800 |
| 2019-2020 | Rackham Interdisciplinary Workshop Grant |
Rackham Graduate School University of Michigan |
$500 |
| 2019-2021 | NIH T32 Bioinformatics Training Program Fellow |
Bioinformatics Graduate Program University of Michigan |
|
| 2017 |
Oswald Research & Creativity Award 2nd place in Biological Sciences |
Office of Undergraduate Research University of Kentucky |
$200 |
| 2017 | Summer Research Grant |
Office of Undergraduate Research University of Kentucky |
$2,000 |
| 2014-2018 | Presidential Scholarship | University of Kentucky | out-of-state full tuition |
| Dates | Title | Institution |
|---|---|---|
| 2018 | Graduated Cum Laude with Departmental Honors in Biology | University of Kentucky |
| 2018 | Biology Undergraduate Research Award Nominee | University of Kentucky |
| 2014-2018 | Lewis Honors College | University of Kentucky |
Last updated: December 22, 2023
* Indicates co-first author.
| Date | Article | Authors | badges |
|---|---|---|---|
| 2023 Aug | Machine Learning Classification by Fitting Amplicon Sequences to Existing OTUs. mSphere | Armour CR, Sovacool KL, Close WL, Topçuoğlu BD, Wiens J, Schloss PD |
|
| 2022 Jul | Intestinal Inflammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides Difficile Colonization in a Mouse Model of Colitis. mBio | Barron MR, Sovacool KL, Abernathy-Close L, Vendrov KC, Standke AK, Bergin IL, Schloss PD, Young VB |
|
| 2022 Feb | OptiFit: An Improved Method for Fitting Amplicon Sequences to Existing OTUs. mSphere | Sovacool KL, Westcott SL, Mumphrey MB, Dotson GA, Schloss PD |
|
| 2022 Jan | Developing and Deploying an Integrated Workshop Curriculum Teaching Computational Skills for Reproducible Research. JOSE | *Lapp Z, *Sovacool KL, Lesniak N, King D, Barnier C, Flickinger M, Krüger J, Armour CR, Lapp MM, Tallant J, Diao R, Oneka M, Tomkovich S, Anderson JM, Lucas SK, Schloss PD |
|
| 2021 Dec | Teaching Python for Data Science: Collaborative Development of a Modular & Interactive Curriculum. JOSE | *Duda M, *Sovacool KL, Farzaneh N, Nguyen VK, Haynes SE, Falk H, Furman KL, Walker LA, Diao R, Oneka M, Drotos AC, Woloshin A, Dotson GA, Kriebel A, Meng L, Thiede SN, Lapp Z, Wolford BN |
|
| 2021 May | Mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. JOSS | *Topçuoğlu BD, *Lapp Z, *Sovacool KL, Snitkin E, Wiens J, Schloss PD |
|
| 2021 Apr | Geography Is More Important than Life History in the Recent Diversification of the Tiger Salamander Complex. PNAS | Everson KM, Gray LN, Jones AG, Lawrence NM, Foley ME, Sovacool KL, Kratovil JD, Hotaling S, Hime PM, Storfer A, Parra-Olea G, Percino-Daniel R, Aguilar-Miguel X, O’Neill EM, Zambrano L, Shaffer HB, Weisrock DW |
|
| 2020 Aug | Ten Simple Rules to Increase Computational Skills among Biologists with Code Clubs. PLoS Comput Biol | Hagan AK, Lesniak NA, Balunas MJ, Bishop L, Close WL, Doherty MD, Elmore AG, Flynn KJ, Hannigan GD, Koumpouras CC, Jenior ML, Kozik AJ, McBride K, Rifkin SB, Stough J, Sovacool KL, Sze MA, Tomkovich S, Topcuoglu BD, Schloss PD |
|
| 2016 Aug | Processing RNA-Seq Data of Plants Infected with Coffee Ringspot Virus. BMC Bioinform | Goodin MM, Farman M, Inocencio H, Jang C, Jaromczyk JW, Moore N, Sovacool KL |
|
N = 9
| Date | Event | Title | Location |
|---|---|---|---|
| Nov 2022 | Bioinformatics Student Research Hour | Predicting C. difficile infection severity from the taxonomic composition of the gut microbiome | University of Michigan |
| Feb 2022 | Seminar for the KG Jebsen Center for Genetic Epidemiology | Intro to git & GitHub | (Virtual) Norwegian University of Science and Technology |
| Mar 2021 | Bioinformatics Student Research Hour | OptiFit: a fast method for fitting amplicon sequences to existing OTUs | (Virtual) University of Michigan |
| Apr 2018 | Systems Biology and Omics Integration Seminar | Developing a Global Homology Analysis for Comparative Genomics | University of Kentucky |
| Date | Event | Title | Location |
|---|---|---|---|
| Jun 2022 | ASM Microbe | Predicting the severity of C. difficile infections from the taxonomic composition of the gut microbiome | Washington, DC |
| Jun 2020 | ASM Microbe | OptiFit: a fast method for fitting amplicon sequences to existing OTUs | Virtual |
| Apr 2018 | Showcase for Undergraduate Scholars | Developing a Global Homology Analysis for Comparative Genomics | University of Kentucky |
| Apr 2018 | National Conference on Undergraduate Research | Developing a Global Homology Analysis for Comparative Genomics | University of Central Oklahoma |
| Apr 2016 | Showcase for Undergraduate Scholars | Processing RNA-seq Reads of Plants Infected with the Coffee Ringspot Virus | University of Kentucky |
| Apr 2016 | UT-KBRIN Bioinformatics Summit | Processing RNA-seq Reads of Plants Infected with the Coffee Ringspot Virus | Cadiz, KY |
| Apr 2015 | Showcase for Undergraduate Scholars | The Effect of Meditation on Performance | University of Kentucky |